The three minors, who cannot be named, are being detained at the youth facility of Durban's Westville prison.
Sivonkaliso Mbili, aged 32, and Vusumuzi Gumede, aged 30, are being detained at Westville prison. The sixth accused, Falakhe Khumalo, was being held in the Chatsworth police station cells.
He was to assist police in the recovery of the murder weapon.
Municipal workers found Desiree Murugan's body at a stadium last month.
The Daily News reported at the time that the 39-year-old had a six-year-old son and worked as a prostitute. She reportedly had a drug habit.
Her head was found in Imfume, on the KwaZulu-Natal south coast.
At the time police spokesperson Colonel Jay Naicker said one of the accused was a traditional healer.
During the group's appearance on Monday, about 70 protesters outside the court called for "witchcrafters and murderers to be burnt alive".